Gene Expression Kinetics
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE11521 | GEO | 2010/03/06
SECONDARY ACCESSION(S): PRJNA106355
REPOSITORIES: GEO
Similar Datasets
Project description:We have taken five different time points of a Yeast culture in exponential grow in rich medium, each one elapsed ten minutes from de previous one (from OD600 0.36 to 0.47). Then, for each time point we have measured the transcription rates (TR) and mRNA amounts (RA) for all the genes using the Genomic run-on (GRO) technique . For each time point we have measured the transcription rates (GRO) with 3 replicates (except for the t2 that only has 2 replicates due to technical problems) and mRNA amounts (cDNA RP) with 3 replicates for all the genes. The data were normalized using a gDNA hybridization for each filter.
2010-03-05 | E-GEOD-11521 | biostudies-arrayexpress
Project description:The effect of Kap120 deletion at transcriptional level was investigated by GRO analysis of the transcription rates (TR) and mRNA levels (RA) genome-wide. mRNA stabilities can be calculated as RA /TR for each gene in all samples.
2022-10-10 | GSE204991 | GEO
Project description:Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F17).
2010-06-19 | E-GEOD-13096 | biostudies-arrayexpress
Project description:Transcription rate (TR) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: Time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F18-F24).
2010-06-19 | E-GEOD-13098 | biostudies-arrayexpress
Project description:Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress Keywords: time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F5-F10). A single DNA genomic hybridization from the same labeling reaction was done on the same macroarrays for normalization.
2008-05-23 | E-GEOD-9663 | biostudies-arrayexpress
Project description:Time courses and RNA isolation. Strains were created that constitutively express fevR (FTT0383) transcript by replacing the endogenous fevR promoter with that of groES, and this gro::fevR region was integrated into either the wild-type, mglA mutant (GB2), or fevR knockout. Overnight cultures of F. novicida strains were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml. Samples were taken throughout the growth curve for RNA isolation and to determine the OD600. Four samples were taken during the growth curve at 2, 4, 6, and 8h for characterization of in gro::fevR bypass experiments. RNA was harvested and a common reference was created by combining equal amounts of RNA from each sample in the experiment. 1ug of RNA from either the samples or common reference was reverse transcribed and samples were labeled with Cy5 (samples) or Cy3 (reference) and hybridized to the Francisella microarray described in Brotcke, Weiss, et al. Infection and Immunity, 2006. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
2009-01-06 | GSE11555 | GEO
Project description:We analyzed the effect of SPT16 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a thermosensitive spt16 point mutant (G132D) mutant at 35 ºC comparing with permisive temperature (30 ºC) and a wt treated in the same way. Cells (wt or spt16 mutant) were grown in SC-ura at 30 ºC to 0.25 OD600. At that time α factor was added and let to stand for 160 min in the same conditions. Then each sample (wt or mutant) was separated in two aliquots. One of them remain at 30ºC and the other was incubated at 35ºC. Both aliquots in the presence of α factor for 1h more. Finally, samples were processed for GRO experiment as described in Garcia-Marinez et al (2004). Three replicates of the whole experiment were done.
2016-01-05 | E-GEOD-64006 | biostudies-arrayexpress
Project description:Time courses and RNA isolation. Overnight cultures of F. novicida strain U112, GB2, and fevR ko (383) were grown in TSB 0.2% cysteine at 37C with shaking and subcultured to an OD600 of 0.01 in 200ml. Samples were taken throughout the growth curve for RNA isolation and to determine the OD600. Five samples were taken during the growth curve at 1, 3, 5, and 7.5h and 10h for characterization of single mutants or at 2, 4, 6, and 8h in gro::fevR bypass experiments. RNA was harvested and a common reference was created from each individual sample. 1ug of either the Sample, or Reference was reverse transcribed and labeled with either Cy5 (samples) or Cy3 (reference) and hybridized to a Francisella microarray previously described in Brotcke, Weiss, et al, Infection and Immunity, 2006. Groups of assays that are related as part of a time series. Age: Red channel represents 1ug of RNA from an individual timepoint Starting OD: Wt, GB2, and FTT0383 (fevR) ko were subbed to an OD of 0.01 in TSB + 0.2% cysteine in 200ml. Keywords: time_series_design
2009-01-06 | GSE11554 | GEO
Project description:Within a GRO experiment, samples for Transcription rate (TR) analysis were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC) and subjected to run-on. Analysis was done in filters also used for RA analysis of aliquots from the same cultures. The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.
2011-04-19 | E-GEOD-24483 | biostudies-arrayexpress
Project description:Within a GRO experiment, samples for mRNA amount (RA) were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC). Analysis was done in filters also used for Transcription rate (TR) analysis of aliquots from the same cultures. The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.
2011-04-19 | E-GEOD-24484 | biostudies-arrayexpress